One of the greatest challenges for analytic metaphysicians concerns the relation of the output of their work with contemporary science. At least for those working under the umbrella of so-called “naturalistic metaphysics”, it is expected that metaphysical theories relate profitably with science. However, it is not even clear how such a relation is to be spelled out in details. We shall begin by enlightening this issue, and separating some distinct kinds of relations that metaphysics may bear with science. As we shall see, one of the greatest expectations comes from the supposed justification a metaphysical theory may derive by being somehow associated with a scientific theory; it is expected that we bridge the gap between metaphysics and epistemology (as encapsulated in science). We shall propose that under a reasonable understanding of the task of metaphysics, there is no way to avoid some metaphysical underdetermination, unless more than mere association with a scientific theory is required. Typically, it is claimed that a decision between com peting metaphysical theories should be made based on their theoretical virtues: simplicity, economy in primitive notions, elegance, perhaps continuity with (part of) common sense, among others. Instead of discussing how theoretical virtues may help metaphysicians, we propose that the obtaining of metaphysical underdetermination is not as easily as it seems when we come to metaphysics associated with science. In fact, it results that it is not always so easy to advance a metaphysical theory consistent with empirical science. As a result, science may help us eliminate theories from the logical space of possibilities;that is, theories inconsistent with science should not be considered as real options for the naturalistic metaphysician, and so, unable to generate more metaphysical underdetermination. In this sense, even though metaphysical theories may not be justified, they may be ruled out by science. This is not as good as it was hoped for, but it is still a kind of improvement of our situation, and, besides, is not far from the situation in science itself. We illustrate how the thesis works with examples from the discussion about individualityin orthodox quantum mechanics.